I have a 91 eclipse GS 1.8 that runs great above or below 3000 RPMs but right at 3000 RPMs it seems like it misses. I have also replaced the computer with on from an automatic transmission where mine is a manual. It also idles a little higher than specs. Could the computer difference cause the problem?

 

You should use the computer meant for your car. I am not sure if that is the problem but it is a very good possibility. The ECU also controls the automatic transmission shift points so it stands to reason that the circuitboard is designed differently than that of the manual tranny type. Good Luck